David Haussler

GBZ-base and GAF-base: Indexed pangenome file formats

The paper introduces GBZ-base and GAF-base, indexed pangenome file formats for efficient subgraph and alignment extraction.

KRAB Zinc Finger Proteins coordinate across evolutionary time scales to battle retroelements

The paper examines the evolutionary arms race between KRAB Zinc Finger Proteins (KZNFs) and retrotransposable elements (RTEs), showing how KZNFs adapt to suppress RTEs over time.

Rapid and efficient analysis of 20,000 RNA-seq samples with Toil

The paper demonstrates Toil's ability to efficiently process 20,000 RNA-seq samples to create a batch-effect-free meta-analysis across five datasets.

The UCSC Genome Browser database: 2016 update

The paper updates the UCSC Genome Browser with new features and data sets, including improved human genome assembly hg38/GRCh38 and new tools for data integration.

Alignathon: A competitive assessment of whole genome alignment methods.

The paper organizes a competitive evaluation of whole genome alignment methods using simulated and real datasets, finding significant accuracy differences between tools and performance variations across evolutionary distances.